We present a search for RR Lyrae stars using the full six-year data set from the Dark Energy Survey (DES) covering ~5,000 sq. deg. of the southern sky. Using a multi-stage multi-variate classification and light curve template-fitting scheme, we identify RR Lyrae candidates with a median of 35 observations per candidate. We detect 6,971 RR Lyrae candidates out to ~335 kpc, and we estimate that our sample is >70% complete at ~150 kpc. We find excellent agreement with other wide-area RR Lyrae catalogs and RR Lyrae studies targeting the Magellanic Clouds and other Milky Way satellite galaxies. We fit the smooth stellar halo density profile using a broken-power-law model with fixed halo flattening (q = 0.7), and we find strong evidence for a break at $R_0 = 32.1^{+1.1}_{-0.9}$ kpc with an inner slope of $n_1 = -2.54^{+0.09}_{-0.09}$ and an outer slope of $n_2 = -5.42^{+0.13}_{-0.14}$. We use our catalog to perform a search for Milky Way satellite galaxies with large sizes and low luminosities. Using a set of simulated satellite galaxies, we find that our RR Lyrae-based search is more sensitive than those using resolved stellar populations in the regime of large ($r_h > 500$ pc), low-surface-brightness dwarf galaxies. A blind search for large, diffuse satellites yields three candidate substructures. The first can be confidently associated with the dwarf galaxy Eridanus II. The second has a similar distance and proper motion to the ultra-faint dwarf galaxy Tucana II but is separated by ~5 deg. The third is close in projection to the globular cluster NGC 1851 but is ~10 kpc more distant and appears to differ in proper motion.
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